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Publications related to 'from sequences'
--- abstract network agreement forest AIC ancestral trait reconstruction approximation APX hard ARG bayesian BIC block realization bootstrap bound branch and bound branch length cactus graph characterization cherry-picking circular split system cluster containment clustering coalescent compressed network compression consensus consistency cophylogeny counting database display set distance between networks distinct-cluster network distinguishability diversity duplication dynamic programming enumeration evaluation explicit network exponential algorithm flat FPT from binary characters from binets from clusters from continuous characters from distances from gene order from multilabeled tree from multistate characters from network from NGS data from quarnets from quartets from rooted trees from species tree from splits from subnetworks from trees from tri-LGT-nets from trinets from triplets from unrooted trees FU-stable network galled network galled tree generation genetically stable network haplotype network haplotyping heuristic History bound HMM hybridization identifiability inapproximability incomplete lineage sorting integer linear programming isomorphism k-reticulated kernelization kth-order reduced network labeling lateral gene transfer level k phylogenetic network LGT network likelihood lineage sorting loss LST distance MASN median network MedianJoining minimal lateral network minimum contradiction minimum number minimum spanning network model selection mrca network MSOL mu distance nearly-stable network NeighborNet nested network netting NNI distance NNI moves normal network NP complete number of vertices optimal realization orchard network orientation outerplanar parental hybridization parsimony partly reduced networks pedigree perfect phylogenetic network phylogeny planar polynomial population genetics Program AdmixTools Program ALE Program Angst Program Arlequin Program ARTNET Program Beagle Program BIMLR Program Bio PhyloNetwork Program BMhyd Program Clustistic Program CMPT Program CombineTrees Program ConsensusNetwork Program constNJ Program CycleKiller Program Dendroscope Program ecceTERA Program EEEP Program FastHN Program FastNet Program FlatNJ Program Frin Program Fylogenetica Program GalledTree Program GraphDTL Program HapBound Program HGT_simul Program HiDe Program HorizStory Program Hybrid-coal Program Hybrid-Lambda Program HybridInterleave Program HybridNET Program HybridNumber Program Hybroscale Program icelu-PhyloNetwork Program IcyTree Program IGNet Program ILPEACE Program JML Program JPrIME-DLTRS Program LatTrans Program LEV1ATHAN Program Lev1Generator Program Level2 Program LGTnetwork Program lingpy Program LNetwork Program MaafB Program Marlon Program MC-Net Program McKiTscH Program Mowgli Program MowgliNNI Program MPNet Program MY CLOSURE Program Nepal Program NetGen Program NetTest Program NetView Program Network Program Notung Program PADRE Program Phangorn Program PhippsNetwork Program PhyloDAG Program PhyloNet Program PhyloNet-HMM Program PhyloNetwork Program PhyloNetworks SNaQ Program PhyloSketch Program PIRN Program PopART Program Prunier Program Pyramids Program QNet Program Quartet Program Quartet Decomposition Program QuartetMethods Program QuartetNet Program QuasiDec Program QuickCass Program RANGER-DTL Program RecMin Program Recodon Program RecPars Program Reticlad Program SAGE Program SAQ-Net Program Serial NetEvolve Program SHRUB Program Simplistic Program Sliding MinPD Program SNSA Program Spectronet Program SplitsTree Program SPNet Program SPRDist Program SuperQ Program SylvX Program T REX Program TCGenerators Program TCS Program TERA Program TerminusEst Program Treeduce Program TreeFix-DTL Program TreeMix Program Treevolve Program TriLoNet Program TripNet Program ultra-Net Program Ultranet Program WeakHierarchies Program Xscape pseudo-polynomial pyramid quasi-median network quasi-reticulation-visible network realization recombination recombination detection reconstruction reduced networks regular network reticulation-visible network reticulogram rigidly displaying SAT semidirected network serial evolutionary networks simulated annealing simulation site consistency software split split decomposition split network SPR distance spread stable-child network stack-free network statistical model statistical parsimony statistical test supernetwork survey tanglegram TBR distance temporal-hybridization number time consistent network tree containment tree sibling network tree-based network tree-child network tree-child sequence tripartition distance triplet distance unicyclic network uniqueness unrooted tree-based network valid network visualization weak hierarchy weakly compatible weakly displaying
abstract-network approximation APX-hard ARG bayesian BIC bootstrap branch-and-bound characterization cluster-containment consensus duplication dynamic-programming enumeration evaluation explicit-network exponential-algorithm FPT from-clusters from-distances from-network from-rooted-trees from-sequences from-species-tree from-splits from-trees from-triplets from-unrooted-trees galled-network galled-tree generation haplotype-network heuristic HMM hybridization inapproximability incomplete-lineage-sorting integer-linear-programming labeling lateral-gene-transfer level-k-phylogenetic-network likelihood loss median-network MedianJoining minimum-number NP-complete parsimony perfect phylogenetic-network phylogeny polynomial population-genetics Program-ALE Program-Beagle Program-GalledTree Program-JPrIME-DLTRS Program-MPNet Program-Nepal Program-NetView Program-Network Program-PhyloDAG Program-PhyloNet Program-PhyloNetworks-SNaQ Program-PopART Program-QuasiDec Program-RecPars Program-SHRUB Program-Sliding-MinPD Program-Spectronet Program-SplitsTree Program-SPNet Program-T-REX Program-TCS Program-TreeFix-DTL quasi-median-network recombination recombination-detection reconstruction semidirected-network serial-evolutionary-networks simulated-annealing simulation software split-network statistical-model statistical-parsimony survey unicyclic-network visualization weakly-displaying
Steven Kelk, Fabio Pardi, Celine Scornavacca and Leo van Iersel. Finding the most parsimonious or likely tree in a network with respect to an alignment. In JOMB, Vol. 78:527-547, 2019.
Keywords: APX hard, from network, from sequences, likelihood, NP complete, parsimony.
Leo van Iersel, Mark Jones and Celine Scornavacca. Improved maximum parsimony models for phylogenetic networks. In SB, Vol. 67(3):518-542, 2018.
Keywords: explicit network, FPT, from sequences, NP complete, parsimony, phylogenetic network, phylogeny, reconstruction, weakly displaying.
Note: https://leovaniersel.files.wordpress.com/2017/12/improved_parsimony_networks.pdf.
Chi Zhang, Huw A. Ogilvie, Alexei J. Drummond and Tanja Stadler. Bayesian Inference of Species Networks from Multilocus Sequence Data. In MBE, Vol. 35(2):504-517, 2018.
Keywords: bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: https://dx.doi.org/10.1093/molbev/msx307.
Dingqiao Wen and Luay Nakhleh. Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data. In SB, Vol. 67(3):439-457, 2018.
Keywords: bayesian, explicit network, from sequences, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
Note: https://doi.org/10.1093/sysbio/syx085.
Christopher Bryant, Mareike Fischer, Simone Linz and Charles Semple. On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic Networks. In JTB, Vol. 417:100-108, 2017.
Keywords: explicit network, from sequences, likelihood, parsimony, phylogenetic network, phylogeny.
Julia Matsieva, Steven Kelk, Celine Scornavacca, Chris Whidden and Dan Gusfield. A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. In TCBB, Vol. 14(2):404-417, 2017.
Keywords: ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny.
Claudia Solís-Lemus, Paul Bastide and Cécile Ané. PhyloNetworks: A Package for Phylogenetic Networks. In MBE, Vol. 34(12):3292-3298, 2017.
Keywords: from sequences, from trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, software.
Note: https://doi.org/10.1093/molbev/msx235.
Cécile Ané. From reconstructing to using phylogenetic networks. Phyloseminar #72, 2017.
Keywords: explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, semidirected network.
Note: https://www.youtube.com/watch?v=PF4j_JOQP0c.
Hussein A. Hejase and Kevin J. Liu. A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. Vol. 17(422):1-12, 2016.
Keywords: abstract network, evaluation, from sequences, phylogenetic network, phylogeny, Program PhyloNet, Program PhyloNetworks SNaQ, reconstruction, simulation, unicyclic network.
Note: http://dx.doi.org/10.1186/s12859-016-1277-1.
Rinku Mathur and Neeru Adlakha. A graph theoretic model for prediction of reticulation events and phylogenetic networks for DNA sequences. In Egyptian Journal of Basic and Applied Sciences, Vol. 3(3):263-271, 2016.
Keywords: from sequences, phylogenetic network, phylogeny, Program T REX.
Note: http://dx.doi.org/10.1016/j.ejbas.2016.07.004.
Mareike Fischer, Leo van Iersel, Steven Kelk and Celine Scornavacca. On Computing The Maximum Parsimony Score Of A Phylogenetic Network. In SIDMA, Vol. 29(1):559-585, 2015.
Keywords: APX hard, cluster containment, explicit network, FPT, from network, from sequences, integer linear programming, level k phylogenetic network, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, Program MPNet, reconstruction, software.
Note: http://arxiv.org/abs/1302.2430.
Quan Nguyen and Teemu Roos. Likelihood-based inference of phylogenetic networks from sequence data by PhyloDAG. In AlCoB15, Vol. 9199:126-140 of LNCS, springer, 2015.
Keywords: BIC, explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software.
Note: http://www.cs.helsinki.fi/u/ttonteri/pub/alcob2015.pdf.
Ward C Wheeler. Phylogenetic network analysis as a parsimony optimization problem. In BMCB, Vol. 16(296):1-9, 2015.
Keywords: explicit network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
Gergely J. Szöllösi, Adrián Arellano Davín, Eric Tannier, Vincent Daubin and Bastien Boussau. Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. In Philosophical Transactions of the Royal Society of London B: Biological Sciences, Vol. 370(1678):1-11, 2015.
Keywords: duplication, from sequences, lateral gene transfer, loss, phylogenetic network, phylogeny, Program ALE, reconstruction.
Note: http://dx.doi.org/10.1098/rstb.2014.0335.
Jessica W. Leigh and David Bryant. PopART: full-feature software for haplotype network construction. In Methods in Ecology and Evolution, Vol. 6(9):1110-1116, 2015.
Keywords: abstract network, from sequences, haplotype network, MedianJoining, phylogenetic network, phylogeny, population genetics, Program PopART, Program TCS, software.
Note: http://dx.doi.org/10.1111/2041-210X.12410.
Sven Herrmann and Vincent Moulton. Computing the blocks of a quasi-median graph. In DAM, Vol. 179:129-138, 2014.
Keywords: abstract network, from sequences, phylogenetic network, phylogeny, polynomial, Program QuasiDec, quasi-median network, reconstruction.
Lavanya Kannan and Ward C Wheeler. Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming. In JCB, Vol. 21(4):303-319, 2014.
Keywords: explicit network, exponential algorithm, from network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
Toggle abstract "Scoring a given phylogenetic network is the first step that is required in searching for the best evolutionary framework for a given dataset. Using the principle of maximum parsimony, we can score phylogenetic networks based on the minimum number of state changes across a subset of edges of the network for each character that are required for a given set of characters to realize the input states at the leaves of the networks. Two such subsets of edges of networks are interesting in light of studying evolutionary histories of datasets: (i) the set of all edges of the network, and (ii) the set of all edges of a spanning tree that minimizes the score. The problems of finding the parsimony scores under these two criteria define slightly different mathematical problems that are both NP-hard. In this article, we show that both problems, with scores generalized to adding substitution costs between states on the endpoints of the edges, can be solved exactly using dynamic programming. We show that our algorithms require O(mpk) storage at each vertex (per character), where k is the number of states the character can take, p is the number of reticulate vertices in the network, m = k for the problem with edge set (i), and m = 2 for the problem with edge set (ii). This establishes an O(nmpk2) algorithm for both the problems (n is the number of leaves in the network), which are extensions of Sankoff's algorithm for finding the parsimony scores for phylogenetic trees. We will discuss improvements in the complexities and show that for phylogenetic networks whose underlying undirected graphs have disjoint cycles, the storage at each vertex can be reduced to O(mk), thus making the algorithm polynomial for this class of networks. We will present some properties of the two approaches and guidance on choosing between the criteria, as well as traverse through the network space using either of the definitions. We show that our methodology provides an effective means to study a wide variety of datasets. © Copyright 2014, Mary Ann Liebert, Inc. 2014."
Yi-Chieh Wu. Computational evolutionary genomics : phylogenomic models spanning domains, genes, individuals, and species. PhD thesis, Massachusetts Institute of Technology, U.S.A., 2014.
Keywords: duplication, from sequences, from species tree, lateral gene transfer, loss, phylogeny, Program TreeFix-DTL, reconstruction.
Note: http://hdl.handle.net/1721.1/87937.
Joel Sjöstrand, Ali Tofigh, Vincent Daubin, Lars Arvestad, Bengt Sennblad and Jens Lagergren. A Bayesian Method for Analyzing Lateral Gene Transfer. In Systematic Biology, Vol. 63(3):409-420, 2014.
Keywords: bayesian, duplication, from rooted trees, from sequences, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program JPrIME-DLTRS, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syu007.
Lavanya Kannan and Ward C Wheeler. Maximum Parsimony on Phylogenetic Networks. In ALMOB, Vol. 7:9, 2012.
Keywords: dynamic programming, explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1186/1748-7188-7-9.
Toggle abstract "Background: Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing phylogenetic trees. Maximum Parsimony is a character-based approach that infers a phylogenetic tree by minimizing the total number of evolutionary steps required to explain a given set of data assigned on the leaves. Exact solutions for optimizing parsimony scores on phylogenetic trees have been introduced in the past.Results: In this paper, we define the parsimony score on networks as the sum of the substitution costs along all the edges of the network; and show that certain well-known algorithms that calculate the optimum parsimony score on trees, such as Sankoff and Fitch algorithms extend naturally for networks, barring conflicting assignments at the reticulate vertices. We provide heuristics for finding the optimum parsimony scores on networks. Our algorithms can be applied for any cost matrix that may contain unequal substitution costs of transforming between different characters along different edges of the network. We analyzed this for experimental data on 10 leaves or fewer with at most 2 reticulations and found that for almost all networks, the bounds returned by the heuristics matched with the exhaustively determined optimum parsimony scores.Conclusion: The parsimony score we define here does not directly reflect the cost of the best tree in the network that displays the evolution of the character. However, when searching for the most parsimonious network that describes a collection of characters, it becomes necessary to add additional cost considerations to prefer simpler structures, such as trees over networks. The parsimony score on a network that we describe here takes into account the substitution costs along the additional edges incident on each reticulate vertex, in addition to the substitution costs along the other edges which are common to all the branching patterns introduced by the reticulate vertices. Thus the score contains an in-built cost for the number of reticulate vertices in the network, and would provide a criterion that is comparable among all networks. Although the problem of finding the parsimony score on the network is believed to be computationally hard to solve, heuristics such as the ones described here would be beneficial in our efforts to find a most parsimonious network. © 2012 Kannan and Wheeler; licensee BioMed Central Ltd."
Cayla McBee. Generalizing Fourier Calculus on Evolutionary Trees to Splits Networks. In ISPAN'12, Pages 149-155, 2012.
Keywords: abstract network, from sequences, phylogenetic network, phylogeny, split network, statistical model.
Toggle abstract "Biologists have been interested in Phylogenetics, the study of evolutionary relatedness among various groups of organisms, for more than 140 years. In spite of this, it has only been in the last 40 years that advances in technology and the availability of DNA sequences have led to statistical, computational and algorithmic work on determining evolutionary relatedness between organisms. One method of determining historical relationships between organisms is to assume a group based evolutionary model and use a discrete Fourier transform. The 1993 paper 'Fourier Calculus on Evolutionary Trees' by L.A. Szekely, M.A. Steel and P.L. Erdos outlines this process. The transform presented in Szekely et al provides an invertible relationship between phylogenetic trees and expected frequencies of nucleotide patterns in nucleotide sequences. This implies that given a set of nucleotide sequences from various organisms it is possible to construct a phylogenetic tree that represents the historical relationships of those organisms. Some scenarios are poorly described by phylogenetic trees and there are biological and statistical reasons for using networks to model phylogenetic relationships. Given this motivation I have generalized Szekely et al's result to apply to a specific type of phylogenetic network known as a splits network. © 2012 IEEE."
Leo van Iersel and Steven Kelk. When two trees go to war. In JTB, Vol. 269(1):245-255, 2011.
Keywords: APX hard, explicit network, from clusters, from rooted trees, from sequences, from triplets, level k phylogenetic network, minimum number, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction.
Toggle abstract "Rooted phylogenetic networks are used to model non-treelike evolutionary histories. Such networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate how they are related. Motivated by the parsimony principle, one often aims to construct a network that contains as few reticulations (non-treelike evolutionary events) as possible. In general, the model chosen influences the minimum number of reticulation events required. However, when one obtains the input data from two binary (i.e. fully resolved) trees, we show that the minimum number of reticulations is independent of the model. The number of reticulations necessary to represent the trees, triplets, clusters (in the softwired sense) and characters (with unrestricted multiple crossover recombination) are all equal. Furthermore, we show that these results also hold when not the number of reticulations but the level of the constructed network is minimised. We use these unification results to settle several computational complexity questions that have been open in the field for some time. We also give explicit examples to show that already for data obtained from three binary trees the models begin to diverge. © 2010 Elsevier Ltd."
Rosalba Radice. A Bayesian Approach to Phylogenetic Networks. PhD thesis, University of Bath, U.K., 2011.
Note: http://opus.bath.ac.uk/25521/.
Alix Boc and Vladimir Makarenkov. Towards an accurate identification of mosaic genes and partial horizontal gene transfers. In NAR, Vol. 39(21):e144, 2011.
Keywords: explicit network, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction.
Note: http://dx.doi.org/10.1093/nar/gkr735.
Toggle abstract "Many bacteria and viruses adapt to varying environmental conditions through the acquisition of mosaic genes. A mosaic gene is composed of alternating sequence polymorphisms either belonging to the host original allele or derived from the integrated donor DNA. Often, the integrated sequence contains a selectable genetic marker (e.g. marker allowing for antibiotic resistance). An effective identification of mosaic genes and detection of corresponding partial horizontal gene transfers (HGTs) are among the most important challenges posed by evolutionary biology. We developed a method for detecting partial HGT events and related intragenic recombination giving rise to the formation of mosaic genes. A bootstrap procedure incorporated in our method is used to assess the support of each predicted partial gene transfer. The proposed method can be also applied to confirm or discard complete (i.e. traditional) horizontal gene transfers detected by any HGT inferring method. While working on a full-genome scale, the new method can be used to assess the level of mosaicism in the considered genomes as well as the rates of complete and partial HGT underlying their evolution. © 2011 The Author(s)."
Hyun Jung Park, Guohua Jin and Luay Nakhleh. Bootstrap-based Support of HGT Inferred by Maximum Parsimony. In BMCEB, Vol. 10:131, 2010.
Keywords: bootstrap, explicit network, from sequences, lateral gene transfer, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2148-10-131.
Toggle abstract "Background. Maximum parsimony is one of the most commonly used criteria for reconstructing phylogenetic trees. Recently, Nakhleh and co-workers extended this criterion to enable reconstruction of phylogenetic networks, and demonstrated its application to detecting reticulate evolutionary relationships. However, one of the major problems with this extension has been that it favors more complex evolutionary relationships over simpler ones, thus having the potential for overestimating the amount of reticulation in the data. An ad hoc solution to this problem that has been used entails inspecting the improvement in the parsimony length as more reticulation events are added to the model, and stopping when the improvement is below a certain threshold. Results. In this paper, we address this problem in a more systematic way, by proposing a nonparametric bootstrap-based measure of support of inferred reticulation events, and using it to determine the number of those events, as well as their placements. A number of samples is generated from the given sequence alignment, and reticulation events are inferred based on each sample. Finally, the support of each reticulation event is quantified based on the inferences made over all samples. Conclusions. We have implemented our method in the NEPAL software tool (available publicly at http://bioinfo.cs.rice.edu/), and studied its performance on both biological and simulated data sets. While our studies show very promising results, they also highlight issues that are inherently challenging when applying the maximum parsimony criterion to detect reticulate evolution. © 2010 Park et al; licensee BioMed Central Ltd."
Fumei Lam, Ryan Tarpine and Sorin Istrail. The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy. In JCB, Vol. 17(6), 2010.
Keywords: explicit network, from sequences, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.brown.edu/~sorin/pdfs/Lam%20the%20imperfect.pdf.
Cuong Than. Inference of parsimonious species phylogenies from multi-locus data. PhD thesis, Rice University, U.S.A., 2010.
Note: http://hdl.handle.net/1911/62177.
Marta Melé, Asif Javed, Marc Pybus, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit and Genographic Consortium. A New Method to Reconstruct Recombination Events at a Genomic Scale. In PLoS Computational Biology, Vol. 6(11):e1001010.1-13, 2010.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1371/journal.pcbi.1001010.
Toggle abstract "Recombination is one of the main forces shaping genome diversity, but the information it generates is often overlooked. A recombination event creates a junction between two parental sequences that may be transmitted to the subsequent generations. Just like mutations, these junctions carry evidence of the shared past of the sequences. We present the IRiS algorithm, which detects past recombination events from extant sequences and specifies the place of each recombination and which are the recombinants sequences. We have validated and calibrated IRiS for the human genome using coalescent simulations replicating standard human demographic history and a variable recombination rate model, and we have finetuned IRiS parameters to simultaneously optimize for false discovery rate, sensitivity, and accuracy in placing the recombination events in the sequence. Newer recombinations overwrite traces of past ones and our results indicate more recent recombinations are detected by IRiS with greater sensitivity. IRiS analysis of the MS32 region, previously studied using sperm typing, showed good concordance with estimated recombination rates. We also applied IRiS to haplotypes for 18 X-chromosome regions in HapMap Phase 3 populations. Recombination events detected for each individual were recoded as binary allelic states and combined into recotypes. Principal component analysis and multidimensional scaling based on recotypes reproduced the relationships between the eleven HapMap Phase III populations that can be expected from known human population history, thus further validating IRiS. We believe that our new method will contribute to the study of the distribution of recombination events across the genomes and, for the first time, it will allow the use of recombination as genetic marker to study human genetic variation. © 2010 Mele ́ et al."
Sagi Snir and Edward Trifonov. A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space. In JCB, Vol. 17(11):1535-1548, 2010.
Keywords: from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://research.haifa.ac.il/~ssagi/published%20papers/JCB-HGT.pdf.
Toggle abstract "Horizontal transfer (HT) is the event of a DNA sequence being transferred between species not by inheritance. This phenomenon violates the tree-like evolution of the species under study turning the trees into networks. At the sequence level, HT offers basic characteristics that enable not only clear identification and distinguishing from other sequence similarity cases but also the possibility of dating the events. We developed a novel, self-contained technique to identify relatively recent horizontal transfer elements (HTEs) in the sequences. Appropriate formalism allows one to obtain confidence values for the events detected. The technique does not rely on such problematic prerequisites as reliable phylogeny and/or statistically justified pairwise sequence alignment. In conjunction with the unique properties of HT, it gives rise to a two-level sequence similarity algorithm that, to the best of our knowledge, has not been explored. From evolutionary perspective, the novelty of the work is in the combination of small scale and large scale mutational events. The technique is employed on both simulated and real biological data. The simulation results show high capability of discriminating between HT and conserved regions. On the biological data, the method detected documented HTEs along with their exact locations in the recipient genomes. Supplementary Material is available online at www.libertonline.com/cmb. Copyright 2010, Mary Ann Liebert, Inc."
Sagi Snir and Tamir Tuller. The NET-HMM approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In JBCB, Vol. 7(4):625-644, 2009.
Keywords: explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model.
Note: http://research.haifa.ac.il/~ssagi/published%20papers/Snir-NET-HMM-JBCB-2009.pdf.
Toggle abstract "Horizontal gene transfer (HGT) is the event of transferring genetic material from one lineage in the evolutionary tree to a different lineage. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Although the prevailing assumption is of complete HGT, cases of partial HGT (which are also named chimeric HGT) where only part of a gene is horizontally transferred, have also been reported, albeit less frequently. In this work we suggest a new probabilistic model, the NET-HMM, for analyzing and modeling phylogenetic networks. This new model captures the biologically realistic assumption that neighboring sites of DNA or amino acid sequences are not independent, which increases the accuracy of the inference. The model describes the phylogenetic network as a Hidden Markov Model (HMM), where each hidden state is related to one of the network's trees. One of the advantages of the NET-HMM is its ability to infer partial HGT as well as complete HGT. We describe the properties of the NET-HMM, devise efficient algorithms for solving a set of problems related to it, and implement them in software. We also provide a novel complementary significance test for evaluating the fitness of a model (NET-HMM) to a given dataset. Using NET-HMM, we are able to answer interesting biological questions, such as inferring the length of partial HGT's and the affected nucleotides in the genomic sequences, as well as inferring the exact location of HGT events along the tree branches. These advantages are demonstrated through the analysis of synthetical inputs and three different biological inputs. © 2009 Imperial College Press."
Sarah C. Ayling and Terence A. Brown. Novel methodology for construction and pruning of quasi-median networks. In BMCB, Vol. 9:115, 2009.
Keywords: abstract network, from sequences, median network, phylogenetic network, phylogeny, quasi-median network, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2105-9-115.
Toggle abstract "BACKGROUND: Visualising the evolutionary history of a set of sequences is a challenge for molecular phylogenetics. One approach is to use undirected graphs, such as median networks, to visualise phylogenies where reticulate relationships such as recombination or homoplasy are displayed as cycles. Median networks contain binary representations of sequences as nodes, with edges connecting those sequences differing at one character; hypothetical ancestral nodes are invoked to generate a connected network which contains all most parsimonious trees. Quasi-median networks are a generalisation of median networks which are not restricted to binary data, although phylogenetic information contained within the multistate positions can be lost during the preprocessing of data. Where the history of a set of samples contain frequent homoplasies or recombination events quasi-median networks will have a complex topology. Graph reduction or pruning methods have been used to reduce network complexity but some of these methods are inapplicable to datasets in which recombination has occurred and others are procedurally complex and/or result in disconnected networks. RESULTS: We address the problems inherent in construction and reduction of quasi-median networks. We describe a novel method of generating quasi-median networks that uses all characters, both binary and multistate, without imposing an arbitrary ordering of the multistate partitions. We also describe a pruning mechanism which maintains at least one shortest path between observed sequences, displaying the underlying relations between all pairs of sequences while maintaining a connected graph. CONCLUSION: Application of this approach to 5S rDNA sequence data from sea beet produced a pruned network within which genetic isolation between populations by distance was evident, demonstrating the value of this approach for exploration of evolutionary relationships."
Tobias Kloepper. Algorithms for the Calculation and Visualisation of Phylogenetic Networks. PhD thesis, Eberhard-Karls-Universität Tübingen, Germany, 2008.
Keywords: from rooted trees, from sequences, from unrooted trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization.
Note: https://publikationen.uni-tuebingen.de/xmlui/handle/10900/49159.
Sagi Snir and Tamir Tuller. Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In WABI08, Vol. 5251:354-368 of LNCS, springer, 2008.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_30.
Toggle abstract "Horizontal Gene Transfer (HGT) is the event of transferring genetic material from one lineage in the evolutionary tree to a different lineage. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Although the prevailing assumption is of complete HGT, cases of partial HGT (which are also named chimeric HGT) where only part of a gene is horizontally transferred, have also been reported, albeit less frequently. In this work we suggest a new probabilistic model for analyzing and modeling phylogenetic networks, the NET-HMM. This new model captures the biologically realistic assumption that neighboring sites of DNA or amino acid sequences are not independent, which increases the accuracy of the inference. The model describes the phylogenetic network as a Hidden Markov Model (HMM), where each hidden state is related to one of the network's trees. One of the advantages of the NET-HMM is its ability to infer partial HGT as well as complete HGT. We describe the properties of the NET-HMM, devise efficient algorithms for solving a set of problems related to it, and implement them in software. We also provide a novel complementary significance test for evaluating the fitness of a model (NET-HMM) to a given data set. Using NET-HMM we are able to answer interesting biological questions, such as inferring the length of partial HGT's and the affected nucleotides in the genomic sequences, as well as inferring the exact location of HGT events along the tree branches. These advantages are demonstrated through the analysis of synthetical inputs and two different biological inputs. © 2008 Springer-Verlag Berlin Heidelberg."
Ernst Althaus and Rouven Naujoks. Reconstructing Phylogenetic Networks with One Recombination. In Proceedings of the seventh International Workshop on Experimental Algorithms (WEA'08), Vol. 5038:275-288 of LNCS, springer, 2008.
Keywords: enumeration, explicit network, exponential algorithm, from sequences, generation, parsimony, phylogenetic network, phylogeny, reconstruction, unicyclic network.
Toggle abstract "In this paper we propose a new method for reconstructing phylogenetic networks under the assumption that recombination events have occurred rarely. For a fixed number of recombinations, we give a generalization of the maximum parsimony criterion. Furthermore, we describe an exact algorithm for one recombination event and show that in this case our method is not only able to identify the recombined sequence but also to reliably reconstruct the complete evolutionary history. © 2008 Springer-Verlag Berlin Heidelberg."
Supriya Munshaw and Thomas B. Kepler. An Information-Theoretic Method for the Treatment of Plural Ancestry in Phylogenetics. In MBE, Vol. 25(6):1199-1208, 2008.
Keywords: explicit network, from sequences, heuristic, phylogenetic network, reconstruction, simulated annealing, software.
Note: http://dx.doi.org/10.1093/molbev/msn066.
Toggle abstract "In the presence of recombination and gene conversion, a given genomic segment may inherit information from 2 distinct immediate ancestors. The importance of this type of molecular inheritance has become increasingly clear over the years, and the potential for erroneous inference when it is not accounted for in the statistical model is well documented. Yet, the inclusion of plural ancestry (PA) in phylogenetic analysis is still not routine. This omission is due to the greater difficulty of phylogenetic inference on general acyclic graphs compared that on with trees and the accompanying computational burden. We have developed a technique for phylogenetic inference in the presence of PA based on the principle of minimum description length, which assigns a cost - the description length - to each network topology given the observed sequence data. The description length combines the cost of poor data fit and model complexity in terms of information. This device allows us to search through network topologies to minimize the total description length. By comparing the best models obtained with and without PA, one can determine whether or not recombination has played an active role in the evolution of the genes under investigation, identify those genes that appear to be mosaic, and infer the phylogenetic network that best represents the history of the alignment. We show that the method performs well on simulated data and demonstrate its application on HIV env gene sequence data from 8 human subjects. The software implementation of the method is available upon request. © The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved."
Cuong Than, Guohua Jin and Luay Nakhleh. Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. In Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'08), Vol. 5267:113-127 of LNCS, springer, 2008.
Keywords: bootstrap, explicit network, from rooted trees, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program Nepal, Program PhyloNet, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg-08.pdf, slides available at http://igm.univ-mlv.fr/RCG08/RCG08slides/Cuong_Than_RCG08.pdf.
Tal Dagan, Yael Artzy-Randrup and William Martin. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. In PNAS, Vol. 105:10039-10044, 2008.
Keywords: from sequences, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1073/pnas.0800679105.
Toggle abstract "Lateral gene transfer is an important mechanism of natural variation among prokaryotes, but the significance of its quantitative contribution to genome evolution is debated. Here, we report networks that capture both vertical and lateral components of evolutionary history among 539,723 genes distributed across 181 sequenced prokaryotic genomes. Partitioning of these networks by an eigenspectrum analysis identifies community structure in prokaryotic gene-sharing networks, the modules of which do not correspond to a strictly hierarchical prokaryotic classification. Our results indicate that, on average, at least 81 ± 15% of the genes in each genome studied were involved in lateral gene transfer at some point in their history, even though they can be vertically inherited after acquisition, uncovering a substantial cumulative effect of lateral gene transfer on longer evolutionary time scales. © 2008 by The National Academy of Sciences of the USA."
Daniel H. Huson. Split networks and Reticulate Networks. In Olivier Gascuel and Mike Steel editors, Reconstructing Evolution, New Mathematical and Computational Advances, Pages 247-276, Oxford University Press, 2007.
Keywords: abstract network, consensus, from rooted trees, from sequences, from splits, from unrooted trees, galled tree, hybridization, phylogenetic network, phylogeny, Program Beagle, Program Spectronet, Program SplitsTree, Program SPNet, recombination, reconstruction, split network, survey.
Note: similar to http://www-ab.informatik.uni-tuebingen.de/research/phylonets/GCB2006.pdf.
Cam Thach Nguyen, Nguyen Bao Nguyen, Wing-Kin Sung and Louxin Zhang. Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem. In TCBB, Vol. 4(3):394-402, 2007.
Keywords: explicit network, from sequences, labeling, NP complete, parsimony, phylogenetic network, phylogeny.
Note: http://www.cs.washington.edu/homes/ncthach/Papers/TCBB2007.pdf.
Dan Gusfield, Vikas Bansal, Vineet Bafna and Yun S. Song. A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. In JCB, Vol. 14(10):1247-1272, 2007.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, Program Beagle, Program GalledTree, recombination, reconstruction, software.
Note: http://www.eecs.berkeley.edu/~yss/Pub/decomposition.pdf.
Yun S. Song, Zhihong Ding, Dan Gusfield, Charles Langley and Yufeng Wu. Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. In JCB, Vol. 14(10):1273-1286, 2007.
Keywords: ARG, from sequences, phylogenetic network, phylogeny, Program SHRUB, reconstruction.
Toggle abstract "Meiotic recombination is a fundamental biological event and one of the principal evolutionary forces responsible for shaping genetic variation within species. In addition to its fundamental role, recombination is central to several critical applied problems. The most important example is "association mapping" in populations, which is widely hoped to help find genes that influence genetic diseases (Carlson et al., 2004; Clark, 2003). Hence, a great deal of recent attention has focused on problems of inferring the historical derivation of sequences in populations when both mutations and recombinations have occurred. In the algorithms literature, most of that recent work has been directed to single-crossover recombination. However, gene-conversion is an important, and more common, form of (two-crossover) recombination which has been much less investigated in the algorithms literature. In this paper, we explicitly incorporate gene-conversion into discrete methods to study historical recombination. We are concerned with algorithms for identifying and locating the extent of historical crossing-over and gene-conversion (along with single-nucleotide mutation), and problems of constructing full putative histories of those events. The novel technical issues concern the incorporation of gene-conversion into recently developed discrete methods (Myers and Griffiths, 2003; Song et al., 2005) that compute lower and upper-bound information on the amount of needed recombination without gene-conversion. We first examine the most natural extension of the lower bound methods from Myers and Griffiths (2003), showing that the extension can be computed efficiently, but that this extension can only yield weak lower bounds. We then develop additional ideas that lead to higher lower bounds, and show how to solve, via integer-linear programming, a more biologically realistic version of the lower bound problem. We also show how to compute effective upper bounds on the number of needed single-crossovers and gene-conversions, along with explicit networks showing a putative history of mutations, single-crossovers and gene-conversions. Both lower and upper bound methods can handle data with missing entries, and the upper bound method can be used to infer missing entries with high accuracy. We validate the significance of these methods by showing that they can be effectively used to distinguish simulation-derived sequences generated without gene-conversion from sequences that were generated with gene-conversion. We apply the methods to recently studied sequences of Arabidopsis thaliana, identifying many more regions in the sequences than were previously identified (Plagnol et al., 2006), where gene-conversion may have played a significant role. Demonstration software is available at www.csif.cs.ucdavis.edu/∼gusfield. © 2007 Mary Ann Liebert, Inc."
Patricia Buendia and Giri Narasimhan. Sliding MinPD: Building evolutionary networks of serial samples via an automated recombination detection approach. In BIO, Vol. 23(22):2993-3000, 2007.
Keywords: from sequences, phylogenetic network, phylogeny, Program Sliding MinPD, recombination, recombination detection, serial evolutionary networks, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btm413.
Toggle abstract "Motivation: Traditional phylogenetic methods assume tree-like evolutionary models and are likely to perform poorly when provided with sequence data from fast-evolving, recombining viruses. Furthermore, these methods assume that all the sequence data are from contemporaneous taxa, which is not valid for serially-sampled data. A more general approach is proposed here, referred to as the Sliding MinPD method, that reconstructs evolutionary networks for serially-sampled sequences in the presence of recombination. Results: Sliding MinPD combines distance-based phylogenetic methods with automated recombination detection based on the best-known sliding window approaches to reconstruct serial evolutionary networks. Its performance was evaluated through comprehensive simulation studies and was also applied to a set of serially-sampled HIV sequences from a single patient. The resulting network organizations reveal unique patterns of viral evolution and may help explain the emergence of disease-associated mutants and drug-resistant strains with implications for patient prognosis and treatment strategies. © The Author 2007. Published by Oxford University Press. All rights reserved."
Galina Glazko, Vladimir Makarenkov, Jing Liu and Arcady Mushegian. Evolutionary history of bacteriophages with double-stranded DNA genomes. In Biology Direct, Vol. 2(36), 2007.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, Program T REX.
Toggle abstract "Background: Reconstruction of evolutionary history of bacteriophages is a difficult problem because of fast sequence drift and lack of omnipresent genes in phage genomes. Moreover, losses and recombinational exchanges of genes are so pervasive in phages that the plausibility of phylogenetic inference in phage kingdom has been questioned. Results: We compiled the profiles of presence and absence of 803 orthologous genes in 158 completely sequenced phages with double-stranded DNA genomes and used these gene content vectors to infer the evolutionary history of phages. There were 18 well-supported clades, mostly corresponding to accepted genera, but in some cases appearing to define new taxonomic groups. Conflicts between this phylogeny and trees constructed from sequence alignments of phage proteins were exploited to infer 294 specific acts of intergenome gene transfer. Conclusion: A notoriously reticulate evolutionary history of fast-evolving phages can be reconstructed in considerable detail by quantitative comparative genomics. © 2007 Glazko et al; licensee BioMed Central Ltd."
Hans-Jürgen Bandelt and Arne Dür. Translating DNA data tables into quasi-median networks for parsimony analysis and error detection. In MPE, Vol. 42(1):256-271, 2007.
Keywords: abstract network, from sequences, parsimony, phylogenetic network, phylogeny, quasi-median network, reconstruction.
Note: http://dx.doi.org/10.1016/j.ympev.2006.07.013.
Toggle abstract "Every DNA data table can be turned into a quasi-median network that faithfully represents the data. We show that for (weighted) condensed data tables the associated network harbors all most parsimonious reconstructions for any tree that connects the sampled haplotypes. Structural features of this network can be computed directly from the data table. The key principle repeatedly used is that the quasi-median network is uniquely determined by the sub-tables for pairs of characters. The translation of a table into a network enhances the understanding of the properties of the data in regard to homoplasy and potential artifacts. The total number of nodes of such a network measures the complexity of the data. In particular, networks that display the results of filter analyses by which hotspot mutations are removed help to detect data idiosyncrasies and thus pinpoint sequencing problems. A pertinent example drawn from human mtDNA illustrates these points. © 2006 Elsevier Inc. All rights reserved."
Hadas Birin, Zohar Gal-Or, Isaac Elias and Tamir Tuller. Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion. In WABI07, Vol. 4645:111-123 of LNCS, springer, 2007.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://safrabio.cs.tau.ac.il/download/Papers/Birin_et_al.pdf.
Yun S. Song. A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree. In TCBB, Vol. 3(2):186-191, 2006.
Keywords: characterization, from sequences, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.eecs.berkeley.edu/~yss/Pub/nasc4gall.pdf.
Guillaume Bourque and Louxin Zhang. Models and Methods in Comparative Genomics. In Chau-Wen Tseng editor, Advances in Computers, Special Volume: Computational Biology, Vol. 68, Elsevier, 2006.
Keywords: from distances, from rooted trees, from sequences, galled tree, phylogenetic network, phylogeny, survey.
Note: http://www.math.nus.edu.sg/~matzlx/papers/CompGen_ZLX.pdf.
Dan Gusfield. On the Full-Decomposition Optimality Conjecture for Phylogenetic Networks. 2005.
Keywords: characterization, explicit network, from sequences, phylogenetic network, reconstruction.
Note: UC Davis Computer Science Technical Report CSE-2005, http://wwwcsif.cs.ucdavis.edu/~gusfield/fullydecomp.pdf.
Dan Gusfield and Vikas Bansal. A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters. In RECOMB05, Vol. 3500:217-232 of LNCS, springer, 2005.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, polynomial, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/gusfieldrecomb.pdf.
Daniel H. Huson and Tobias Kloepper. Computing recombination networks from binary sequences. In ECCB05, Vol. 21(suppl. 2):ii159-ii165 of BIO, 2005.
Keywords: from sequences, phylogenetic network, phylogeny, recombination.
Note: http://dx.doi.org/10.1093/bioinformatics/bti1126.
Toggle abstract "Motivation:Phylogenetic networks are becoming an important tool in molecular evolution, as the evolutionary role of reticulate events, such as hybridization, horizontal gene transfer and recombination, is becoming more evident, and as the available data is dramatically increasing in quantity and quality. Results: This paper addresses the problem of computing a most parsimonious recombination network for an alignment of binary sequences that are assumed to have arisen under the 'infinite sites' model of evolution with recombinations. Using the concept of a splits network as the underlying datastructure, this paper shows how a recent method designed for the computation of hybridization networks can be extended to also compute recombination networks. A robust implementation of the approach is provided and is illustrated using a number of real biological datasets. © The Author 2005. Published by Oxford University Press. All rights reserved."
Rune Lyngsø, Yun S. Song and Jotun Hein. Minimum Recombination Histories by Branch and Bound. In WABI05, Vol. 3692:239-250 of LNCS, springer, 2005.
Keywords: ARG, branch and bound, from sequences, minimum number, Program Beagle, recombination, reconstruction, software.
Note: http://www.cs.ucdavis.edu/~yssong/Pub/WABI05-239.pdf.
Wei-Shun Su, Tso-Ching Lee and Yaw-Ling Lin. Efficient Algorithms for Constructing Phylogenetic Networks with Restricted Recombinations. In NCS05, Pages 1-7, 2005.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.168.6735.
Dan Gusfield, Satish Eddhu and Charles Langley. Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. In JBCB, Vol. 2(1):173-213, 2004.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/exfinalrec.pdf.
Toggle abstract "A phylogenetic network is a generalization of a phylogenetic tree, allowing structural properties that are not tree-like. In a seminal paper, Wang et al.1 studied the problem of constructing a phylogenetic network, allowing recombination between sequences, with the constraint that the resulting cycles must be disjoint. We call such a phylogenetic network a "galled-tree". They gave a polynomial-time algorithm that was intended to determine whether or not a set of sequences could be generated on galled-tree. Unfortunately, the algorithm by Wang et al.1 is incomplete and does not constitute a necessary test for the existence of a galled-tree for the data. In this paper, we completely solve the problem. Moreover, we prove that if there is a galled-tree, then the one produced by our algorithm minimizes the number of recombinations over all phylogenetic networks for the data, even allowing multiple-crossover recombinations. We also prove that when there is a galled-tree for the data, the galled-tree minimizing the number of recombinations is "essentially unique" . We. also note two additional results: first, any set of sequences that can be derived on a galled tree can be derived on a true tree (without recombination cycles), where at most one back mutation per site is allowed; second, the site compatibility problem (which is NP-hard in general) can be solved in polynomial time for any set of sequences that can be derived on a galled tree. Perhaps more important than the specific results about galled-trees, we introduce an approach that can be used to study recombination in general phylogenetic networks. This paper greatly extends the conference version that appears in an earlier work.8 PowerPoint slides of the conference talk can be found at our website. © Imperial College Press."
Dan Gusfield, Satish Eddhu and Charles Langley. The fine structure of galls in phylogenetic networks. In INCOMP, Vol. 16(4):459-469, 2004.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/informs.pdf.
Toggle abstract "A phylogenetic network is a generalization of a phylogenetic tree, allowing properties that are not tree-like. With the growth of genomic data, much of which does not fit ideal tree models, there is greater need to understand the algorithmics and combinatorics of phylogenetic networks (Posada and Crandall 2001, Schierup and Hein 2000). Wang et al. (2001) studied the problem of constructing a phylogenetic network for a set of n binary sequences derived from the all-zero ancestral sequence, when each site in the sequence can mutate from zero to one at most once in the network, and recombination between sequences is allowed. They showed that the problem of minimizing the number of recombinations in such networks is NP-hard, but introduced a special case of the problem, i.e., to determine whether the sequences could be derived on a phylogenetic network where the recombination cycles are node-disjoint. Wang et al. (2001) provide a sufficient, but not a necessary test, for such solutions. Gusfield et al. (2003, 2004) gave a polynomial-time algorithm that is both a necessary and sufficient test. In this paper, we study in much more detail the fine combinatorial structure of node-disjoint cycles in phylogenetic networks, both for purposes of insight into phylogenetic networks and to speed up parts of the previous algorithm. We explicitly characterize all the ways in which mutations can be arranged on a disjoint cycle, and prove a strong necessary condition for a set of mutations to be on a disjoint cycle. The main contribution here is to show how structure in the phylogenetic network is reflected in the structure of an efficiently-computable graph, called the conflict graph. The success of this approach suggests that additional insight into the structure of phylogenetic networks can be obtained by exploring structural properties of the conflict graph."
Dan Gusfield, Satish Eddhu and Charles Langley. Efficient reconstruction of phylogenetic networks with constrained recombination. In CSB03, Pages 363-374, 2003.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/ieeefinal.pdf.
Kirill Kryukov and Naruya Saitou. Netview: Application Software for Constructing and Visually Exploring Phylogenetic Networks. In Genome Informatics, Vol. 14:280-281, 2003.
Keywords: from sequences, phylogenetic network, phylogeny, Program NetView, visualization.
Note: http://www.jsbi.org/journal/GIW03/GIW03SS06.pdf.
Lusheng Wang, Kaizhong Zhang and Louxin Zhang. Perfect phylogenetic networks with recombination. In SAC01, Pages 46-50, 2001.
Keywords: from sequences, galled tree, NP complete, perfect, phylogenetic network, phylogeny, polynomial, recombination, reconstruction.
Note: http://dx.doi.org/10.1145/372202.372271.
Hans-Jürgen Bandelt, Vincent Macaulay and Martin Richards. Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. In MPE, Vol. 16:8-28, 2000.
Keywords: from sequences, from splits, median network, phylogenetic network, phylogeny, reconstruction.
Note: http://www.stats.gla.ac.uk/~vincent/papers/speedy.pdf.
Toggle abstract "Molecular data sets characterized by few phylogenetically informative characters with a broad spectrum of mutation rates, such as intraspecific control-region sequence variation of human mitochondrial DNA (mtDNA), can be usefully visualized in the form of median networks. Here we provide a step-by-step guide to the construction of such networks by hand. We improve upon a previously implemented algorithm by outlining an efficient parametrized strategy amenable to large data sets, greedy reduction, which makes it possible to reconstruct some of the confounding recurrent mutations. This entails some postprocessing as well, which assists in capturing more parsimonious solutions. To simplify the creation of the resulting network by hand, we describe a speedy approach to network construction, based on a careful planning of the processing order. A coalescent simulation tailored to human mtDNA variation in Eurasia testifies to the usefulness of reduced median networks, while highlighting notorious problems faced by all phylogenetic methods in this context. Finally, we discuss two case studies involving the comparison of characters in the two hypervariable segments of the human mtDNA control region in the light of the worldwide control-region sequence database, as well as additional restriction fragment length polymorphism information. We conclude that only a minority of the mutations that hit the second segment occur at sites that would have a mutation rate comparable to those at most sites in the first segment. Discarding the known 'noisy' sites of the second segment enhances the analysis. (C) 2000 Academic Press."
Mark Clement, David Posada and Keith A. Crandall. TCS: a computer program to estimate gene genealogies. In MOLE, Vol. 9:1657-1659, 2000.
Keywords: from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, reconstruction, software, statistical parsimony.
Note: http://darwin.uvigo.es/download/papers/08.tcs00.pdf.
Toggle abstract [No abstract available]
Alan R. Templeton, Keith A. Crandall and Charles F. Sing. A Cladistic Analysis of Phenotypic Associations With Haplotypes Inferred From Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation. In GEN, Vol. 132:619-633, 2000.
Keywords: from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, recombination, reconstruction, statistical parsimony.
Note: http://www.genetics.org/cgi/content/abstract/132/2/619.
Bin Ma, Lusheng Wang and Ming Li. Fixed topology alignment with recombination. In DAM, Vol. 104:281-300, 2000.
Keywords: approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.40.7759.
Toggle abstract "Background: Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50.Results: Here we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations.Conclusions: Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):1635-1656, TCBB 10(1):18-25, SIDMA 28(1):49-66) and are publicly available. We also apply our methods to real data. © 2014 van Iersel et al.; licensee BioMed Central Ltd."
Hans-Jürgen Bandelt, Peter Forster and Arne Röhl. Median-joining networks for inferring intraspecies phylogenies. In MBE, Vol. 16(1):37-48, 1999.
Keywords: from sequences, median network, MedianJoining, Program Network, reconstruction, software.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/16/1/37.
John Kececioglu and Dan Gusfield. Reconstructing a history of recombinations from a set of sequences. In DAM, Pages 239-260, 1998.
Keywords: from sequences, NP complete, polynomial, recombination, reconstruction.
Note: http://citeseer.ist.psu.edu/76600.html.
Bin Ma, Lusheng Wang and Ming Li. Fixed topology alignment with recombination. In CPM98, Vol. 1448:174-188 of LNCS, springer, 1998.
Note: http://dx.doi.org/10.1007/BFb0030789.
John Kececioglu and Dan Gusfield. Reconstructing a history of recombinations from a set of sequences. In SODA94, Pages 471-480, 1994.
Note: http://portal.acm.org/citation.cfm?id=314626#.
Jotun Hein. A heuristic method to reconstruct the history of sequences subject to recombination. In JME, Vol. 36(4):396-405, 1993.
Keywords: explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny, Program RecPars, recombination, recombination detection, software.
Note: http://dx.doi.org/10.1007/BF00182187.


The Association "Ukrautoprom" has a stable, yet flexible structure, consisting of the enterprises of the Ukrainian automotive industry in the person of their directors.
The Association "Ukrautoprom" is headed by the President Mykhailo Borysovych Reznik.
The Presidium of the Association which manages actual operation.
The supreme body of the Association is the Member gathering.
The status of the Association member can be obtained by juridical persons, that are admitted into its membership in accordance with the decision of the Council of the Association. Every member of the Association has one voice at the Member gathering of the Association. Full members of the Association have the right of a decisive voice at the Member assembly of the Association; the associated members have the right of a consultative voice.


The approach to Summer Lake on Hwy. 31 in south central Oregon feels a bit like you're entering a Hollywood movie set for a modern-day Western. They call this part of the state Oregon's Outback, and local names have a distinct pioneer charm. You can camp at Coffee Pot Flats, for instance, or have your supper at the Dinner Bell Diner. The actual "town" of Summer Lake boasts one gas station/general store, one small white community church, a handful of houses, the Department of Fish and Wildlife station, and a former Army barracks turned resort. No stoplights needed here because you're in and out of town in less than a minute. But treasures await those willing to stick around.
A side street with the idyllic name, Thousand Springs Lane, hints at the storehouse of beauty surrounding you. Stands of billowy cottonwoods skirt the highway, a 7000'volcanic ridge covered in pine forest rises on your right, and a dramatic sweep of sky covers an enormous shallow lake like an overturned bowl of robin's egg blue. People show up here for all kinds of reasons. Scientists study layers of lava flow that mark geologic time in this high desert basin, fisherman follow the abundant trout streams, retirees take the road less traveled on their way to California. And then there are folks like us. That huge body of wetlands draws us this Memorial Day weekend in late May. We have come for the birds.
Hundreds of species congregate in this inland marsh to rest and refuel on their way to and from Alaska and Central America. Thousands of shorebirds breed here every spring. Bird names fall from the lips like one-word prayers: avocet, ibis, bufflehead, phalarope, willet, shrike. If you come in mid-March, the locals tell us, you will witness a sight (and sound) that is something to behold, the migration of tens of thousands of snow geese. Sadly, there is always the unfortunate misfit who didn't get the message. One solitary snow goose sat in the middle of the marsh on our visit looking utterly lost and forlorn. His tribe had moved on without him, his fate remained uncertain.
I joke that I married the original Boy Scout. In addition to his tying complex knots and making a great campfire quicker than anyone I know, my husband is a skilled birder. Though he grew up in what is now clearly urban sprawl, Northern New Jersey, he once scouted the woods and marshes of his native state — binoculars, field guide, and notepad in tow — at sixteen. I, on the other hand, only admired birds from afar, growing up as I did in many states with my nose usually deep in a book. And while I remember marveling at paintings by John James Audubon in the pages of National Geographic, I learned only the names of common backyard birds we all encounter, nothing more. Until now.
Our first morning out in the marsh brings unexpected delights. We run into a trio of birders from Terrebonne, a couple hours north. Two are retired biology teachers, one of whom has been coming to this lake for twenty-five years. They are serious about their pastime, judging by the gear they sport, but also quite friendly. They alert us to an old barn far out in the middle of the marsh where a pair of fledgling great-horned owls perch together on top of the roof. From a distance they look like two large, fluffy gray kittens huddled side by side for comfort. They are absolutely adorable. And they watch our every move with impossible 180-degree head turns. Swallows flit in and out of the eaves bringing more mud to patch their fragile, powdery homes. One of the many things I learn is that the average swallow weighs all of 2 oz. Good thing, or their tiny houses would collapse. Big Mama owl, wary of the attention we're paying to her babies, keeps a close eye on us from inside the barn.
Summer Lake Wildlife Refuge was created in 1944 and is still managed by the state as both a refuge and a reserve for duck hunting, rather a unique example of cooperation between groups who often fight turf battles over environmental and recreational rights. The lake is what's known as a hemi-marsh, meaning 50% water and 50% vegetation. Eight miles of winding gravel road loops through the marsh, plus long walking dykes and several small foot bridges that span the canals and inner pools. Huge underground springs feed the lake from snow runoff cascading down Winter Ridge.
The weekend before Summer Lake, I was up in Seattle visiting my oldest sister and enjoying a solo literary getaway, attending a wonderful reading and reception for poet Scott Cairns, sponsored by Image. I wore my favorite little black dress and new snappy green sandals. While there, I ate in two fashionable restaurants, and I rode the Amtrak Cascades coming and going. I thoroughly enjoyed my Big City romp, living as I do in a small, quaint college town of 55,000. But Summer Lake offers me something neither of those places ever can — the expanse of wilderness. Every day we surround ourselves with manmade structures and agendas and priorities set by us, the human beings. When you venture into those wetlands you are reminded again that an entire world happens out there without you, every day, every season of the year. Staggering, beautiful, abundant life. The peace of wild things.
One of the short videos my husband took at Summer Lake has no narration to it. It's simply the common sounds of the marsh: the raucous ducks, the ratchety marsh wrens, the plaintive cranes, the whistling terns, the shrill hawks, and the softly hooting doves. I would've been content to pull up a camp chair and just listen for an hour, thermos of coffee in hand. I wasn't really looking for another hobby, but it seems I've found a compatible one in birding. We recorded eighty-one species in two and a half days. Not bad for an occasional birder and wannabe sidekick. Hang around with some veteran birders and you'll soon learn their secrets. I have a long way to go to catch up with my husband, but I can tell the difference (without binoculars) between a red-tail hawk soaring high overhead and a turkey vulture, just by the shape of their wings and how they fly. I now recognize a Lazuli Bunting from a Western bluebird, even though they both have blue coats and reddish breasts. I know a crow's tail is flat and a raven's is shaped more like a spoon. Ravens are larger, and crows are their archrivals.
Another little known secret to share: when my husband and I take these wilderness trips together we don't bicker and nitpick like we often do at home. We're less grumpy, more genial. Everything slows down; we are not the center of the universe. Our homegrown cares diminish in significance and our impatience with one another's quirks, well-noted after long years of marriage, slough off. We're already planning our next trip for the end of September. Fall migration in full display. No duck hunters yet, not until October. Maybe we'll camp this time and wake to savannah sparrows just outside our tent flaps. Maybe we'll make our goal of 100 species, not that anyone else takes note. It's as if we, too, by returning to a simpler, gentler habitat, transform into another species. Not forever, but for a time, as the poet puts it, we rest in the grace of the world.
Please read a note from the Art House America Board about the future of the blog.
Mary Van Denend writes poems and essays from her home in Oregon's lush Willamette Valley. She is the author of Watermarks (Finishing Line Press, 2013) and is a regular contributor to the Art House America Blog. A graduate of Calvin College and Seattle Pacific University's MFA in Creative Writing program, she works with disabled people in Supported Employment.


There, I've done it again: I found another usage guide at our local (Dutch!) charity shop Het Warenhuis.
How did the book end up in the Netherlands? There is no ownership inscription unfortunately, so we won't know who the former owner was. But more seriously, who is the author, Harry Blamires?
Googling for him brought me to Wikipedia, where it can be read that he was born in 1916, and that he is a (now retired) theologian, literary critic and novelist. And also that he was formerly head of the English department at King Alfreds College (Winchester University today) in Winchester, in English. But the entry doesn't mention the title of my new book.
The HUGE database includes another book by Harry Blamires, The Queen's English, published in 1994 by Bloomsbury. My book came out even later, in 1998, published by BCA (Book Club Associates: thanks to Tim Waller for pointing this out!). Were both books written by the same Harry Blamires whose first publication, according to Wikipedia, was a novel called Devil's Hunting Ground (1954), who wrote guides through James Joyce's Ulysses and T.S. Eliot's Four Quartets, as well publishing a book called Recovering the Christian Mind: Meeting the Challenge of Secularism (1988)?
Please help us identify the author of The Cassell Guide to Common Errors in English and of The Queen's English. Ideally of course, we would like to get in touch with the author himself.
Thanks to Harry Blamires' son, Cyprian Blamires, for telling us that his father is now 98!
This entry was posted in biography, usage guide and tagged Harry Blamires. Bookmark the permalink.
8 Responses to Who is Harry Blamires?
Regarding BCA, are you absolutely sure it stands for Burnidge Cassell Associates here? Maybe it does, but from the title of the book, I'd have thought the publisher was Cassell, which was swallowed up by Orion a few years ago. You probably already know this, but BCA quite often stands for Book Club Associates, a mail-order book club that produces its own editions of books, with its own name on the spine (or at least pays the publisher to do so).
I'm not familiar with the author, but I see from AbeBooks that he's also the author of The Penguin Guide to Plain English and Compose Yourself and Write Good English. There's something on the Penguin website about him.
Thank you for your point, you are quite right to doubt me. I did think of Book Club Associates at first, but in my copy of Partridge's Usage and Abusage, their name is spelled out in full. Also, the logos are different. Thank you for the reference to the Penguin website. I'll have a look. But we are still waiting for a reply from the author himself!
Tim, I concede defeat (as they say): you are absolutely right. I just looked up the Book Club Associates in Wikipedia, where a different logo is given from the one you describe in your comment, and which I was familiar with. It is the same one which occurs on the title page of my copy of Blamires' book! Thanks for your help in this.
The Penguin website suggests that it is the same man.
I have just come across your discussion of Harry Blamires.
Currently aged 98 and living in a Home.
Many thanks for getting in touch with us, Cyprian: apologies for the error in the post, which has been corrected. I hope you will tell your father that we admire his work, and that his book on usage plays a role in our research on usage guides.
Dear Cyprian, Purely by chance I came across your name in this 2014 article and recalled meeting you in Oxford, probably around 1968. You were a very good friend of my late brother, Adrian, who you probably know died in his mid 30s as the result of an RTA.
Anyway, strange how something from the past can crop up.


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Gartner Identity & Access Management Summit
6 – 7 March 2023 | London, U.K.
Nick Tuffs
Nick is currently the Service Owner for Access Governance within Cyber and Information Security at UBS, a global team of more than 150 people accountable for ensuring UBS colleagues can get the access they need, while ensuring compliance with regulatory needs. Prior to joining UBS 4 years ago, he led significant IAM implementation projects at a major UK Bank and Global Telecoms provider. Initially, Nick started his career as an IT Auditor at a Big 4 Accountancy firm before turning to consultancy on numerous client IAM projects.
Tuesday, 07 March, 2023 / 02:00 PM - 02:30 PM GMT
Case Study Presentation by UBS: Project Cadmus: Slaying the Monsters!
Cadmus was a Greek Hero, renowned for slaying monsters. UBS has over the course of several decades created several "monsters" through the entitlement management tools that were custom built for the needs of specific business areas. UBS needed to reduce complexity for their business users that was impacting productivity, while also finding ways to improve their security posture and ability to meet compliance mandates. With multiple siloed solutions increasing operational and infrastructure costs, the need for change was obvious. However, doing all this required ambition and innovation as these tools touched every corner of the organization. UBS had attempted this before several years ago with a vendor product but without success, so many people asked - what is different this time? This session will go through the differential factors that have led to Cadmus being a success.

redpajama_set_name: RedPajamaCommonCrawl


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Kennedy Funding inks $1 million loan for 22-acre project in Tulsa
The site of a planned mixed-use development at 36th Street North and Martin Luther King Jr. Boulevard in Tulsa, Oklahoma — Courtesy: Kennedy Funding
Kennedy Funding has closed on more than $1 million in financing to help pave the way for a planned mixed-use development in Tulsa, Oklahoma.
The direct private lender, which is based in Englewood Cliffs, on Friday announced the $1.05 million loan to Alfresco Group LLC. The borrower will use the proceeds for site preparation, working capital and soft costs for site construction for the project, which will develop 22 acres of raw land into multifamily housing, retail space and a boutique hotel.
Kennedy noted that the developer, whose site is located at 36th Street North and Martin Luther King Jr. Boulevard in Tulsa, closed the loan only 10 days after accepting its offer.
"Traditional lenders often take months to close loans because they are deeply risk-averse and slow-moving," said Kevin Wolfer, CEO of Kennedy Funding. "Because our dedicated team does not have the same restrictions as a bank, when our team performed its due diligence, we were able to see the project for what it will be, as opposed to what it isn't."
Located just north of Gilcrease Expressway, the property is comprised of three adjacent parcels that were purchased in three stages over the past two years, Kennedy said. The firm noted that the site is minutes from Osage Casino and four miles from downtown Tulsa, while also close to shopping and tourism destinations and area universities.
The Tulsa International Airport and several major highways — including routes 75, 412 and 64 and Interstates 44 and 244 — are easily accessible from the property.
"This development will offer not just new housing opportunities for college students, young professionals, couples and families, but additional shopping opportunities and a luxurious hotel located a quick drive from all of Tulsa's biggest attractions," Wolfer said.
Tags Alfresco Group LLC kennedy funding Tulsa
L+M sees new office space as key complement to apartments, retailers at historic Newark tower
Kislak closes Jersey Shore investment sales totaling $8.5 million


A $200,000 contract to study the feasibility of safety improvements favoring bicyclists and pedestrians along two Concord roadways was approved this week by the City Council.
Most of the funding, more than $177,000, will be paid for by a Sustainable Transportation Planning grant from Caltrans. The rest of the money will coming from Measure Q sales tax funds, according to a report prepared by city staff.
The study will create maps, collect data, develop alternative designs and coordinate community workshops with a focus on improving safety and access for bicyclists and pedestrians on Galindo Street and designated segments of Willow Pass and Cowell roads in the vicinity of the Concord BART station.
After putting out a request for proposals, city staff selected Alta Planning + Design, a firm with experience on previous projects of this nature, including Concord's Bicycle, Pedestrian and Safe Routes Transit Plan in 2016.
I wonder if everyone followed the laws that are already in place, would there be such a concern?
It's very sad that some people refuse the be responsible, law-abiding citizens and that government feels it has to step in and protect some people from themselves.
A government that has to protect people from themselves is a government that will ultimately control every aspect of people lives.
Seriously? With all the road needing repair, homeless needs and so many more important needs of the city, you want to spend $200k on a study for bicyclists? Shameful! Get real with what is needed!!!
Awesome! Cyclists (and pedestrians) need protection. Maybe dedicated (protected) bike lanes?
Or, maybe just ban bicyclists because they cannot seem to follow the laws.
Here comes more green around town.
What about repairing our roads? Another year passes and lots of roads in disrepair.
$200,000 of our tax money for a report that bikes are good for us though not always safe that'll be copy/pasted from similar reports for other cities? We won't even be getting design plans for bikeways out of this.
As nearly all of it is a Caltrans grant that means all of us are paying for this one. While Concord's Measure Q is a sales tax thing, meaning no direct out of pocket for Concord residents, I suspect the $23,000 of measure Q money being used for this report could be better spent.
While they have an office in Oakland, Alta Planning + Design is not a local company. They are based in Portland, OR. Thus, much of that money will not remain local.
Just another totally unnecessary luxury.
"I can't drink muh beverage unless it has bubbles, duhrrr".
What ever became of the plan to change the two merge lanes at Treat Blvd & 680 and turn them into Bike lanes!!!
ALTERNATIVE CONCEPT is nuts!!! remove the dedicated "right turn and merge lane" from the Treat Off ramp!
40,000 cars a day and they are going to drastically limit traffic in order to accommodate 42 bikes a day that would use that lane. Don't forget if the the bikes move over 2 blocks south the Iron Horse Trail has no traffic and a dedicated tunnel under the freeway.
THE TAIL IS WAGING THE DOG!!!
Every bike you see on the road is one less car wearing out the road and one more parking space available for my car.
Not really. Most cyclers are hobbyists, they leave home and return without stopping.
Underground tunnels for cyclists, now there's an idea!
Anytime the term "feasibility study" is used, you can be assured a lot of money will be spent and little will get done.
How much you want to bet its city councils own children that just graduated and need jobs that got this project, nepotism at its finest with the tax payers money. 200k to draw some maps, signs and study! this is madness!
This is badly needed. Right now, you have to ride on the sidewalk to get from BART to any of the shopping destinations in Concord – and the sidewalks are even more busted than the roadways! Adding simple bike safety features, like green paint and pop-up barriers, adds very little to the overall cost of repaving streets.
The DMV regulates the laws for bicycles in CA.
Bicyclists have the same rights and responsibilities as motorists and are subject to the same rules and regulations. You can find more detail at the CA DMV website.
As it would be for a car, bicycles are illegal on sidewalks and don't have the privilege of a pedestrian.
I think if more people followed the law, there would be far less trouble on the roadway.
sidewalk if the local jurisdiction allows it.
the sidewalk and signs are posted saying so.
"must" ride on the Ygnacio Valley Rd. sidewalk.
A Transportation Study was paid for and started before the turn of the century and released in 2002 but not implemented. Then a new study was started in 2012 and released in 2016. http://cityofconcord.org/pdf/projects/transit/sr2t042016.pdf – Why do we need to study this more rather than start spending the money start some of these fixes? There's a map that says existing bike routes. An absolute Joke. Concord Blvd from Ayers to Clayton City limits is a bike Route, No signage, no complete shoulder, no lane markings. Olive Dr is an existing route but you have to go around the creek on either Clayton Rd or Concord Blvd. No signage or signs even when it's an existing route even though can't ride or even walk it. Wilson is existing route, same non marked route. There are a number "Existing" Class II & III on the figure 2.2 that don't exist nearly 3 years after the last report. According to the "existing" map except for the Bailey Path there are only two Class l Shared use paths in Concord and none of them were created by the city of Concord. The Canal and Iron Horse trail are part of the East Bay Regional Park system. When you drop your kids or grand kids off at school check out the bike lanes or Class 1 walking access. Concord is all about cars, not people and the proof is in two decades of studies and now another study… It going to take more than "Bike Concord" on Facebook to create people friendly paths that connect in Concord.
In other words, bicycles, which pay no road taxes, will be taking more lanes from motor vehicles which do pay road taxes and are already facing horribly congested traffic. And contrary to all of the disinformation and hype…few people commute via bike. Most of the bicyclists on our streets are indulging in recreation. This being California, those who pay the taxes will again take it in the shorts for those who pay none. Bike lanes on bridges are a great example of this Socialist/Progressive theft.
Lets put bike lanes in like they did on Grant. That aren't used. I have been bumped twice, almost knocked down once by bikes while walking from 1655 Grant to downtown.
Granted it was only one month, and 180 miles….but I used my bike for one month as sole transportation in Concord. Doable…only fear was of theft from Safeway on Willow Pass. Ended up bringing bike in store. Did not make manager happy. No comment was mafe to all animal humans, or thieves of beer and groceries, but me. I could assemble a bike from parts left on Safeway's bike racks. Safeway could employ Bike Concord members as bike valets….Win win..
At least Safeway stores have bicycle racks. The post offices in Walnut Creek and Pleasant hill do not have any racks. I once biked over to the Social Security building at the corner of Ygnacio and Civic. They have a bike rack but it was around the side of the building in an area with no pedestrian traffic. The building is next to a homeless encampment. I locked my bike to a bench next to the front door.
Cyclists don't pay taxes? We do ride bikes regularly for fitness and recreation, but also have a late model suv, truck and fifth wheel. Registration alone is over $1,500/yr.
We all support parks, boat ramps and a variety of public facilities that we may not personally use, We also get annoyed with traffic and inadequate roads, but the bicycles have always been here. We may have ridden bikes to school as kids, but see today's traffic as too crazy for our kids, or grandkids to do the same ride. So, maybe bikes are not the only problem.
Concord City Council is aiming for its "World Class" designations with its fixation on bicycling, promoting it as a major form of transportation in the area … "World Class" like China or India.
Here are the results: we need wider sidewalks and dedicated bike lanes.
Here's the reality: if people walking paid attention and people riding bikes followed the rules of the road, they would be perfectly safe!
The goal of making over our society into a bike/pedestrian friendly utopia will never be accomplished by expensively tearing out what's already built or by luring inexperienced riders into the middle of car traffic with the Siren Call of green pavement paint.
New development, both commercial and residential, is green lit and allowed to be built without building bike/pedestrian access. I see housing subdivisions being built where the kids wouldn't be able to leave their neighborhood without being driven. I see shopping center renovations where in the interest of squeezing in a few more parking spaces, the private sidewalks no longer connect to the the city sidewalks – pedestrians have to walk in traffic to access the shopping center, or hike over the landscaping. Won't work in a wheelchair.
Then maybe in twenty or thirty years we can pay "consultants" $200,000 to deliver us the amazing insight that bikes are good. I'll do it for free. "Bikes are good.". You're welcome.
This is madness. The gubmit's left hand doesn't know or care what the gubmit's right hand is doing. Stop approving new construction that completely disregards pedestrian and bicycle access. We can't afford to build things wrong, and then thirty years later tear up roads for expensive realignments. That $200,00 could fix a lot of potholes.


text:
Hacking Into Diagnostics
New survey finds nearly 80% of consumers think vehicle hacking will be a frequent problem in the near future.
The vulnerabilities of vehicle hacking have made an impression on car owners and shoppers, and nearly 80 percent say it will be a frequent problem within the next three years or less, according to a new survey by Kelley Blue Book. Awareness of the recent Jeep Cherokee hacking incident is very high, and nearly half of respondents said they would keep this event in mind when buying or leasing their next car. Moreover, the majority of consumers do not think there will ever be a permanent solution to the problem of vehicle hacking.
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"Technology offers a wide range of enhanced convenience for today's new vehicle buyers, but it also offers the increasing potential for unauthorized access and control," said Karl Brauer, senior analyst for Kelley Blue Book. "Cyber-security is still a relatively new area of specialization for automakers, but it's one they need to take seriously to ensure they are ahead of the curve. If automotive engineers find themselves playing catch-up in this field, it could have disastrous results for both consumers and the industry. According to Kelley Blue Book's latest survey, while few consumers consider vehicle hacking a major problem today, many feel it will be a real threat in the next one-to-three years. Consumers also are highly skeptical that a comprehensive solution to prevent vehicle hacking can ever be developed, though an overwhelming majority would be willing to pay for hack-proof vehicle security if it existed."
Key highlights from Kelley Blue Book's Vehicle Hacking Vulnerability Survey include:
Awareness and Concerns about Vehicle Hacking
72 percent said they are aware of the recent Jeep Cherokee hacking incident.
41 percent said they will consider this recent vehicle hacking incident when buying/leasing their next car.
78 percent said vehicle hacking will be a frequent problem in the next three years or less.
33 percent classified vehicle hacking as a "serious" problem; 35 percent classified it as a "moderate" problem.
58 percent do not think there will ever be a permanent solution to vehicle hacking.
41 percent think pranking is the most common reason for hacking a vehicle; 37 percent think theft is the most common reason for hacking a vehicle.
Responsibility and Preferred Methods for Vehicle Hacking Notification/Fix
The vast majority of respondents view vehicle manufacturers as most responsible to secure a vehicle from hacking, and most would prefer to get a security patch installed in-person at a dealership right away.
81 percent think the vehicle manufacturer is most responsible to secure a vehicle from hacking; only 11 percent consider themselves most responsible to secure a vehicle from hacking, and 5 percent see it as the responsibility of their wireless provider.
64 percent would prefer to go into a dealership to get a vehicle's security patch installed; only 24 percent would prefer to do it wirelessly, and a mere 12 percent would prefer to have the software mailed so they could install it themselves.
47 percent said they would go to a dealership "immediately" if they knew they had to install a security patch to protect their vehicle from hacking; 31 percent said "within a week," and 17 percent said "within a month."
44 percent would prefer to be notified via mail, and 41 percent would prefer to be notified via email, in the event their vehicle was recalled. Only 11 percent preferred notification via a phone call, and 5 percent preferred text.
52 percent indicated they would be willing to pay for a monthly subscription to ensure that their vehicle would be completely protected from hacking, with $8 being the average respondents would be willing to pay each month.
Kelley Blue Book fielded the Vehicle Hacking Vulnerability Survey from July 24-27, 2015, and the survey had 1,134 respondents. Surveys were completed by members of Kelley Blue Book's Blue Ribbon Panel, an online community for vehicle owners and shoppers who are invited to share opinions that provide valuable and timely insights.
Article courtesy of BodyShop Business.
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Flowerpot VP7 Pendant Light
£340.00 RRP
2 weeks production time
Delivery to United Kingdom in 5-9 days
Technical sheet (.pdf)
Debuted in 1968, Flowerpot's playful design remains enduringly popular
The Flowerpot, a vividly coloured lamp with a rounded pendant that hangs from the semi-domed upper shade, embodies the experimental attitude that Danish designer Verner Panton took to home items.
As a disciple of Arne Jacobsen and Poul Henningsen, Panton always sought to prioritize the functionalism of furniture design. But he proved far less conventional when it came to his use of new materials and colour, working with psychologists to better understand the role that colour played in shaping the psychology of an environment. "Most people spend their lives living in dreary, grey-beige conformity, mortally afraid of using colours," he once said – an observation that went on to define his approach to interiors.
The Flowerpot endures as an iconic example of his legacy. Created in 1968, it quickly became a visual symbol of the freewheeling Flower Power movement and the peace and love ideology that its followers espoused. Perhaps this was because it melded the precision of Danish design to an attitude of individualism, remaining practical while still playful; functional yet fun.
"As one of the greats of Danish design, Verner Panton revolutionized the way in which we think about interior design" &Tradition founder and CEO Martin Kornbek Hansen says. "More than fifty years after it was created, the Flowerpot continues to lend its unconventional credentials to homes around the world."
A beloved part of &Tradition's collection since 2010, the Flowerpot is now available in a new mid-sized option designed to fit perfectly over a dining table. Two additional colours – red-brown and light blue – have also been added to the range.
Verner Panton started out as a painter before studying architecture at the Royal Academy of Fine Arts in Copenhagen. After an apprenticeship with architect / designer Arne Jacobsen, Panton pursued a path in furniture and interior design, where he became famous for his avant-garde designs. Such as chairs with no legs and a sofa placed vertically against the wall. In the 60's and 70's, his passion for designing entire environments led to immersive interiors featuring his hypnotic patterns and futuristic designs for furniture, lighting, wallpapers, posters and rugs. Panton's pioneering use of materials, colours and shapes earned him a reputation as a visionary.
The Flowerpot lamp became emblematic of the Flower Power peace movement during the 60's. With its range of vivid colours, it is just as synonymous with modernity now as it was when launched in 1968. Panton's Topan lamp - the first he ever designed - is the Flowerpot's little sister, made up of a simple semi-sphere that can be configured in clusters. "Panton's provocative use of materials, geometric shapes and psychedelic colours set him apart from his contemporaries," notes Martin Kornbek Hansen. "Our portfolio of &Tradition products wouldn't be complete without this endearing example from this evangelist of radical design."
Craft meets art. Function meets form. Material meets potential.